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| Status |
Public on Feb 01, 2017 |
| Title |
The significance of different algorithms in transcriptome analysis of leukemic cells with rearranged MLL (RNA-seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
This study shows how the way by which the RNA-Seq data is analyzed affects the resulting gene expression profile. Three parameters were explored: the RNA-Seq analysis algorithm pipeline (cufflinks – Cuffdiff 2 or HTSeq & DESeq), sequencing depth and sequencing protocol: single or paired end, 100 or 50 bases. For comparison, the same samples were processed by gene microarrays.
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| Overall design |
RNA-Seq and gene microarray was conducted on four acute lymphoblastic leukemia (ALL) precursor B cell lines, two lines carrying the chromosome translocation t(4;11) in which the human MLL gene is rearranged, and two lines lacking this abnormality.
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| Contributor(s) |
Leshkowitz D, Canaani E |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Feb 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Dena Leshkowitz |
| E-mail(s) |
dena.leshkowitz@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Bioinformatics Unit, Life Sciences Core Facilities
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| Street address |
P.O.B. 26
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE54654 |
The significance of different algorithms in transcriptome analysis of leukemic cells with rearranged MLL |
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| Relations |
| BioProject |
PRJNA237246 |
| SRA |
SRP036166 |
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